A significant proportion of HIV-1 infected children, adolescents, and adults, who are treated with combinations of protease and reverse transcriptase inhibitors, develop sustained improvement in clinical outcomes, reconstitution of CD4 T ceils, and restoration of immune function [immune success], even though plasma virus persists at high levels, which would indicate a poor prognosis in untreated patients [viral failure]. Discordant [viral failure/immune success] therapy responses occur in as many as 40% of infected children and adolescents and can persist for years. The hypothesis underlying the proposed research is that discordant therapy responses involve multiple factors, including a drug-induced genetic bottleneck; accumulation of mutations in viral gag-pol regions; impaired fitness for replication in thymic tissue and lymphocytes to account for reconstitution of CD4 T cell numbers; and continued virus production by cells, such as long-lived macrophages, to account for persistently high levels of plasma viremia. In Preliminary Studies, virus infection within peripheral lymphocytes from discordant response patients were reduced following therapy to levels that were com parable to patients with optimal viral suppression. Replication by viruses with post-therapy gag-PR regions from discordant response patients was diminished in cultures of lymphocytes, but maintained in macrophages, indicating that fitness of viruses evolving in discordant response patients under the selective pressure of therapy differ from pretherapy viruses. Three specific aims, which will use innovative combinations of cellular and molecular approaches to determine mechanisms involved in development and persistence of discordant responses, are proposed: 1. To evaluate impact on intrathymic and extrathymic T cell development by continued replication of post-therapy viruses in discordant response patients, 2. To identify genetic determinants in gag/PR regions from post-therapy viruses that contribute to cell-lineage specific fitness, and 3. To identify an impact on global genetic networks in different cell lineages by protease inhibitors or protease genotypes. The proposed studies are significant for understanding fundamental mechanisms of interactions between viruses, which replicate under the selective pressures of inhibitors, and host cells, and are critical for design of novel therapeutic strategies to treat HIV-infected patients who fail combination antiretroviral therapy.